Thermodynamics, formation dynamics and structural correlations in the bulk amorphous phase of the phase-field crystal model

We investigate bulk thermodynamic and microscopic structural properties of amorphous solids in the framework of the phase-field crystal (PFC) model. These are metastable states with a non-uniform density distribution having no long-range order. From extensive numerical simulations we determine the distribution of free energy density values in varying size amorphous systems and also the point-to-set correlation length, which is the radius of the largest volume of amorphous one can take while still having the particle arrangements within the volume determined by the particle ordering at the surface of the chosen volume. We find that in the thermodynamic limit, the free energy density of the amorphous tends to a value that has a slight dependence on the initial state from which it was formed -- i.e.\ it has a formation history dependence. The amorphous phase is observed to form on both sides of the liquid linear-stability limit, showing that the liquid to amorphous transition is first order, with an associated finite free energy barrier when the liquid is metastable. In our simulations this is demonstrated when noise in the initial density distribution is used to induce nucleation events from the metastable liquid. Depending on the strength of the initial noise, we observe a variety of nucleation pathways, in agreement with previous results for the PFC model, and which show that amorphous precursor mediated multi-step crystal nucleation can occur in colloidal systems.Comment: 13 pages, 16 figure

Brucella epididymo-orchitis: A single-center experience with a review of the literature

Brucella epididymo-orchitis (BEO) is a rare complication of brucellosis. Despite the high incidence of brucellosis in developing countries, few case series on BEO are available. This study focuses on the clinical presentations, diagnosis, and treatment of BEO with a review of the literature. This study included consecutive BEO patients diagnosed and treated at Smart Health Tower between 2021 and 2023. The required data were retrospectively collected from patients' profiles. The BEO diagnosis was established through scrotal Doppler ultrasound in cases with a positive Rose Bengal test and positive IgG and IgM results for brucellosis, in addition to scrotal pain and swelling. This study included 11 cases whose ages ranged from 22 to 55 years. Most of the cases presented with testicular pain (72.7%), followed by fever (63.6%) and arthralgia (63.6%). The right side (54.5%) was slightly more affected than the left side (45.5%). The major abnormal laboratory finding was an elevated C-reactive protein (82%). The treatment was conservative, in which a combination of gentamicin, doxycycline, and rifampicin was administered to the patients for about 6-8 weeks. One case underwent an orchiectomy due to the abscess formation. All the patients responded well to the treatment, with no recurrence. In the Middle East, brucellosis remains a concerning infectious disease. Early diagnosis, aimed at preventing abscess formation and other complications, takes first priority to avoid invasive interventions

Quantum mechanics simulation of Cadmium(II) tripeptide complexes

Cadmium detection in aqueous medium is an important step in attempt to avoid human exposure to the extremely toxic metal. It is believed that one of the significant qualitative detection processes of cadmium(II) can be performed using a biosensor with the help of small peptides as the biological material. The current issue is that proper peptides to capture cadmium(II) are still unknown, since there is not enough information about the interaction between the metal ion and most of the small peptides in literature. Quantum mechanics methods, such as Density Functional Theory (DFT), can be employed to understand the electronic interaction between cadmium(II) and the peptides. Minnesota 06 functional (M06) in combination with Default 2 triple zeta plus polarization (Def2TZVP) basis set was denoted as the best method among those, which were employed in this research to describe properties of several cadmium complexes, such as Cd-S bond length and S-Cd-S bond angle. For this purpose, data on cadmium(II) benzenthiolato was extracted from Cambridge Structural Database (CSD) and compared to the computed data on the same molecule achieved theoretically using Becke Three Parameter Hybrid Functional in combination with Double zeta split-valence plus polarization basis set (B3LYP/DGDZVP) and M06/Def2TZVP. The results from the second method yielded 2.66% of errors for Cd-S bond lengths and 2.87% of errors for S-Cd-S bond angles, while in the presence of DGDZVP basis set in combination with B3LYP the errors rose up to 5.17% in Cd-S bond lengths and 4.90% in S-Cd-S bond angles. Cadmium(II) complexes with the small peptides, such as dipeptide, tripeptide and tetrapeptide were optimized employing M06/Def2TZVP and Polarizable Continuum Method (PCM) to determine the peptide length effect on the Cd-Sbinding energy. Cd-S binding energy in the tripeptide, if compared with the dipeptide and the tetrapeptide, was bigger as much as 12.62 kJ and 5.82 kJ respectively. Therefore, Cd-S binding energy of different tripeptide sequences were screened by fixing cysteine in the terminals and changing the middle amino acid to each one of the twenty essential amino acids. The optimization was performed in vacuum using B3LYP/DGDZVP and M06/Def2TZVP methods. The procedures were repeated using PCM, in which water was chosen as the solvent, to investigate dielectric effect of water molecules on the Cd-S moiety. Cd-S binding energy of Cysteine-Proline-Cysteine (CPC) is the highest, if compared to the other observed nineteen tripeptides with the binding energies of 285.98 kJ in the presence of PCM using M06/Def2TZVP. The computed bond lengths between the metal ion and the sulfur atoms, using M06/Def2TZVP, are between 2.353 Å to 2.476 Å in vacuum, and 2.434 Å to 2.451 Å with PCM. Thus, CPC peptide could serve as biological material in the cadmium(II) biosensor application

Numerical modelling of amorphous solids: A classical density functional theory based approach

In this thesis, the Phase-Field Crystal (PFC) model is used to describe amorphous solid materials. These stationary states are metastable minima of the free energy, that are characterised by a non-uniform density distribution displaying no long-range order. In the introductory part of the thesis, first we give a summary of the thermodynamics and kinetics of phase transitions, which is followed by an introduction to the Classical Density Functional Theory (DFT) and its dynamical extension (DDFT), in which the physical state of the matter is characterised by a spatiotemporal scalar field, the density distribution. This part of the thesis ends with the derivation of the PFC model from the DDFT, which is then used to investigate the bulk thermodynamic and microscopic structural properties of amorphous solids. In the next part of the thesis, we present and analyse the results of extensive numerical simulations. First, we determine the distribution of the free energy density in the amorphous state for various system sizes, and show that the amorphous state can be modelled as a collection of uncorrelated finite-sized domains. We calculate the typical size (correlation length) of these correlated regions.</p

Thermodynamics, formation dynamics and structural correlations in the bulk amorphous phase of the phase-field crystal model

We investigate bulk thermodynamic and microscopic structural properties of amorphous solids in the framework of the phase-field crystal (PFC) model. These are metastable states with a non-uniform density distribution having no long-range order. From extensive numerical simulations we determine the distribution of free energy density values in varying size amorphous systems and also the point-to-set correlation length, which is the radius of the largest volume of amorphous one can take while still having the particle arrangements within the volume determined by the particle ordering at the surface of the chosen volume. We find that in the thermodynamic limit, the free energy density of the amorphous tends to a value that has a slight dependence on the initial state from which it was formed – i.e. it has a formation history dependence. The amorphous phase is observed to form on both sides of the liquid linear-stability limit, showing that the liquid to amorphous transition is first order, with an associated finite free energy barrier when the liquid is metastable. In our simulations this is demonstrated when noise in the initial density distribution is used to induce nucleation events from the metastable liquid. Depending on the strength of the initial noise, we observe a variety of nucleation pathways, in agreement with previous results for the PFC model, and which show that amorphous precursor mediated multi-step crystal nucleation can occur in colloidal systems.</p